mass - molecular masses and isotope distributions¶

Summary¶

This module defines general functions for mass and isotope abundance calculations. For most of the functions, the user can define a given substance in various formats, but all of them would be reduced to the Composition object describing its chemical composition.

Classes¶

Composition - a class storing chemical composition of a substance.

Unimod - a class representing a Python interface to the Unimod database (see pyteomics.mass.unimod for a much more powerful alternative).

Mass calculations¶

calculate_mass() - a general routine for mass / m/z calculation. Can calculate mass for a polypeptide sequence, chemical formula or elemental composition. Supplied with an ion type and charge, the function would calculate m/z.

fast_mass() - a less powerful but much faster function for polypeptide mass calculation.

fast_mass2() - a version of fast_mass that supports modX notation.

Isotopic abundances¶

isotopic_composition_abundance() - calculate the relative abundance of a given isotopic composition.

most_probable_isotopic_composition() - finds the most abundant isotopic composition for a molecule defined by a polypeptide sequence, chemical formula or elemental composition.

isotopologues() - iterate over possible isotopic conposition of a molecule, possibly filtered by abundance.

Data¶

nist_mass - a dict with exact masses of the most abundant isotopes.

std_aa_comp - a dict with the elemental compositions of the standard twenty amino acid residues, selenocysteine and pyrrolysine.

std_ion_comp - a dict with the relative elemental compositions of the standard peptide fragment ions.

std_aa_mass - a dict with the monoisotopic masses of the standard twenty amino acid residues, selenocysteine and pyrrolysine.

Composition.__init__(*args, **kwargs)[source]¶

A Composition object stores a chemical composition of a substance. Basically it is a dict object, in which keys are the names of chemical elements and values contain integer numbers of corresponding atoms in a substance.

The main improvement over dict is that Composition objects allow addition and subtraction.

A Composition object can be initialized with one of the following arguments: formula, sequence, parsed_sequence or split_sequence.

If none of these are specified, the constructor will look at the first positional argument and try to build the object from it. Without positional arguments, a Composition will be constructed directly from keyword arguments.

If there’s an ambiguity, i.e. the argument is both a valid sequence and a formula (such as ‘HCN’), it will be treated as a sequence. You need to provide the ‘formula’ keyword to override this.

Warning

Be careful when supplying a list with a parsed sequence or a split sequence as a keyword argument. It must be obtained with enabled show_unmodified_termini option. When supplying it as a positional argument, the option doesn’t matter, because the positional argument is always converted to a sequence prior to any processing.

Parameters:

formula (str, optional) – A string with a chemical formula.
sequence (str, optional) – A polypeptide sequence string in modX notation.
parsed_sequence (list of str, optional) – A polypeptide sequence parsed into a list of amino acids.
split_sequence (list of tuples of str, optional) – A polypeptyde sequence parsed into a list of tuples (as returned be pyteomics.parser.parse() with split=True).
aa_comp (dict, optional) – A dict with the elemental composition of the amino acids (the default value is std_aa_comp).
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).
ion_type (str, optional) – If specified, then the polypeptide is considered to be in the form of the corresponding ion.

Composition.mass(**kwargs)[source]¶

Calculate the mass or m/z of a Composition.

Parameters:

average (bool, optional) – If True then the average mass is calculated. Note that mass is not averaged for elements with specified isotopes. Default is False.
charge (int, optional) – If not 0 then m/z is calculated. See also: charge_carrier.
charge_carrier (str or dict, optional) –
Chemical group carrying the charge. Defaults to a proton, “H+”. If string, must be a chemical formula, as supported by the Composition formula argument, except it must end with a charge formatted as “[+-][N]”. If N is omitted, single charge is assumed. Examples of charge_carrier: “H+”, “NH3+” (here, 3 is part of the composition, and + is a single charge), “Fe+2” (“Fe” is the formula and “+2” is the charge). .. note :: charge must be a multiple of charge_carrier charge.

If dict, it is the atomic composition of the group. In this case, the charge can be passed separately as carrier_charge or it will be deduced from the number of protons in charge_carrier.
carrier_charge (int, optional) –
Charge of the charge carrier group (if charge_carrier is specified as a composition dict).

Note

charge must be a multiple of charge_charge.
mass_data (dict, optional) – A dict with the masses of the chemical elements (the default value is nist_mass).
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).
ion_type (str, optional) – If specified, then the polypeptide is considered to be in the form of the corresponding ion. Do not forget to specify the charge state!
absolute (bool, optional) –
If True (default), the m/z value returned will always be positive, even for negatively charged ions.

Note

absolute only applies when charge is negative. The mass can still be negative for negative compositions.

Returns:

mass

Return type:

float

class pyteomics.mass.mass.Unimod(source='http://www.unimod.org/xml/unimod.xml')[source]¶

Bases: object

A class for Unimod database of modifications. The list of all modifications can be retrieved via mods attribute. Methods for convenient searching are by_title and by_name. For more elaborate filtering, iterate manually over the list.

Note

See pyteomics.mass.unimod for a new alternative class with more features.

__init__(source='http://www.unimod.org/xml/unimod.xml')[source]¶

Create a database and fill it from XML file retrieved from source.

Parameters:: source (str or Path or file, optional) – A file-like object, file name or a URL to read from.

by_id(i)[source]¶

Search modifications by record ID. If a modification is found, it is returned. Otherwise, KeyError is raised.

Parameters:: i (int or str) – The Unimod record ID.
Returns:: out – A single modification dict.
Return type:: dict

by_name(name, strict=True)[source]¶

Search modifications by name. If a single modification is found, it is returned. Otherwise, a list will be returned.

Parameters:

name (str) – The full name of the modification(s).
strict (bool, optional) – If False, the search will return all modifications whose full name contains name, otherwise equality is required. True by default.

Returns:

out – A single modification or a list of modifications.

Return type:

dict or list

by_title(title, strict=True)[source]¶

Search modifications by title. If a single modification is found, it is returned. Otherwise, a list will be returned.

Parameters:

title (str) – The modification title.
strict (bool, optional) – If False, the search will return all modifications whose title contains title, otherwise equality is required. True by default.

Returns:

out – A single modification or a list of modifications.

Return type:

dict or list

property mass_data¶: Get element mass data extracted from the database

property mods¶: Get the list of Unimod modifications

pyteomics.mass.mass.calculate_mass(*args, **kwargs)[source]¶

Calculates the monoisotopic mass of a polypeptide defined by a sequence string, parsed sequence, chemical formula or Composition object.

One or none of the following keyword arguments is required: formula, sequence, parsed_sequence, split_sequence or composition. All arguments given are used to create a Composition object, unless an existing one is passed as a keyword argument.

Note that if a sequence string is supplied and terminal groups are not explicitly shown, then the mass is calculated for a polypeptide with standard terminal groups (NH2- and -OH).

Warning

Be careful when supplying a list with a parsed sequence. It must be obtained with enabled show_unmodified_termini option.

Parameters:

formula (str, optional) – A string with a chemical formula.
sequence (str, optional) – A polypeptide sequence string in modX notation.
proforma (str, optional) – A polypeptide sequeence string in ProForma notation, or a pyteomics.proforma.ProForma object.
parsed_sequence (list of str, optional) – A polypeptide sequence parsed into a list of amino acids.
composition (Composition, optional) – A Composition object with the elemental composition of a substance.
aa_comp (dict, optional) – A dict with the elemental composition of the amino acids (the default value is std_aa_comp).
average (bool, optional) – If True then the average mass is calculated. Note that mass is not averaged for elements with specified isotopes. Default is False.
charge (int, optional) – If not 0 then m/z is calculated: the mass is increased by the corresponding number of proton masses and divided by charge.
charge_carrier (str or dict, optional) –
Chemical group carrying the charge. Defaults to a proton, “H+”. If string, must be a chemical formula, as supported by the Composition formula argument, except it must end with a charge formatted as “[+-][N]”. If N is omitted, single charge is assumed. Examples of charge_carrier: “H+”, “NH3+” (here, 3 is part of the composition, and + is a single charge), “Fe+2” (“Fe” is the formula and “+2” is the charge).

Note

charge must be a multiple of charge_carrier charge.

If dict, it is the atomic composition of the group. In this case, the charge can be passed separately as carrier_charge or it will be deduced from the number of protons in charge_carrier.
carrier_charge (int, optional) –
Charge of the charge carrier group (if charge_carrier is specified as a composition dict).

Note

charge must be a multiple of charge_charge.
mass_data (dict, optional) – A dict with the masses of the chemical elements (the default value is nist_mass).
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).
ion_type (str, optional) – If specified, then the polypeptide is considered to be in the form of the corresponding ion. Do not forget to specify the charge state!
absolute (bool, optional) –
If True (default), the m/z value returned will always be positive, even for negatively charged ions.

Note

absolute only applies when charge is negative. The mass can still be negative for negative compositions.

Returns:

mass

Return type:

float

pyteomics.mass.mass.fast_mass(sequence, ion_type=None, charge=None, **kwargs)[source]¶

Calculate monoisotopic mass of an ion using the fast algorithm. May be used only if amino acid residues are presented in one-letter code.

Parameters:

sequence (str) – A polypeptide sequence string.
ion_type (str, optional) – If specified, then the polypeptide is considered to be in a form of corresponding ion. Do not forget to specify the charge state!
charge (int, optional) – If not 0 then m/z is calculated: the mass is increased by the corresponding number of proton masses and divided by z.
absolute (bool, optional) – If True (default), the m/z value returned will always be positive, even for negatively charged ions.
mass_data (dict, optional) – A dict with the masses of chemical elements (the default value is nist_mass).
aa_mass (dict, optional) – A dict with the monoisotopic mass of amino acid residues (default is std_aa_mass);
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).

Returns:

mass – Monoisotopic mass or m/z of a peptide molecule/ion.

Return type:

float

pyteomics.mass.mass.fast_mass2(sequence, ion_type=None, charge=None, **kwargs)[source]¶

Calculate monoisotopic mass of an ion using the fast algorithm. modX notation is fully supported.

Parameters:

sequence (str) – A polypeptide sequence string.
ion_type (str, optional) – If specified, then the polypeptide is considered to be in a form of corresponding ion. Do not forget to specify the charge state!
charge (int, optional) – If not 0 then m/z is calculated: the mass is increased by the corresponding number of proton masses and divided by z.
absolute (bool, optional) – If True (default), the m/z value returned will always be positive, even for negatively charged ions.
mass_data (dict, optional) – A dict with the masses of chemical elements (the default value is nist_mass).
aa_mass (dict, optional) – A dict with the monoisotopic mass of amino acid residues (default is std_aa_mass).
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).

Returns:

mass – Monoisotopic mass or m/z of a peptide molecule/ion.

Return type:

float

pyteomics.mass.mass.fragment_series(peptide, ion_types=('b', 'y'), maxcharge=1, aa_mass=None, mass_data=None, ion_comp=None) → dict[str, dict[str, float]][source]¶

Generate fragment m/z and name series for ProForma and modX sequences.

Parameters:

peptide (str) – A modX or ProForma sequence.
ion_types (Container, optional) – Ion types to be considered. Default is (‘b’, ‘y’).
maxcharge (int, optional) – Maximum charge state for fragment ions. Default is 1.
aa_mass (dict, optional) – A dictionary of amino acid residue masses. Only used for modX sequences. Default is std_aa_mass.
mass_data (dict, optional) – A dictionary of element masses. Only used for modX sequences. Default is nist_mass.
ion_comp (dict, optional) – A dictionary defining ion compositions. Only used for modX sequences. Default is std_ion_comp.

Returns:

out – Nested dictionary with ion types as first-level keys, and individual ion labels as second-level keys. The values are the corresponding m/z values.

Return type:

dict

Examples

>>> fragments = fragment_series('PEPTIDE')
>>> fragments['b']['b1+']
97.05276384885
>>> list(fragments['b'].keys())
['b1+', 'b2+', 'b3+', 'b4+', 'b5+', 'b6+']
>>> fragments = fragment_series('PEPTIDE', maxcharge=2)
>>> list(fragments['b'].keys())[:4]
['b1+', 'b2+', 'b3+', 'b4+']
>>> fragments['b']['b1++']
48.52974924125
>>> fragments = fragment_series('PEP[+15.994915]TIDE')  # ProForma format
>>> fragments['b']['b1+']
97.05276384885

pyteomics.mass.mass.isotopic_composition_abundance(*args, **kwargs)[source]¶

Calculate the relative abundance of a given isotopic composition of a molecule.

Parameters:

formula (str, optional) – A string with a chemical formula.
composition (Composition, optional) – A Composition object with the isotopic composition of a substance.
mass_data (dict, optional) – A dict with the masses of chemical elements (the default value is nist_mass).

Returns:

relative_abundance – The relative abundance of a given isotopic composition.

Return type:

float

pyteomics.mass.mass.isotopologues(*args, **kwargs)[source]¶

Iterate over possible isotopic states of a molecule. The molecule can be defined by formula, sequence, parsed sequence, or composition. The space of possible isotopic compositions is restrained by parameters elements_with_isotopes, isotope_threshold, overall_threshold.

Parameters:

formula (str, optional) – A string with a chemical formula.
sequence (str, optional) – A polypeptide sequence string in modX notation.
parsed_sequence (list of str, optional) – A polypeptide sequence parsed into a list of amino acids.
composition (Composition, optional) – A Composition object with the elemental composition of a substance.
report_abundance (bool, optional) – If True, the output will contain 2-tuples: (composition, abundance). Otherwise, only compositions are yielded. Default is False.
elements_with_isotopes (container of str, optional) – A set of elements to be considered in isotopic distribution (by default, every element has an isotopic distribution).
isotope_threshold (float, optional) – The threshold abundance of a specific isotope to be considered. Default is 5e-4.
overall_threshold (float, optional) – The threshold abundance of the calculateed isotopic composition. Default is 0.
aa_comp (dict, optional) – A dict with the elemental composition of the amino acids (the default value is std_aa_comp).
mass_data (dict, optional) – A dict with the masses of chemical elements (the default value is nist_mass).

Returns:

out – Iterator over possible isotopic compositions.

Return type:

iterator

pyteomics.mass.mass.most_probable_isotopic_composition(*args, **kwargs)[source]¶

Calculate the most probable isotopic composition of a peptide molecule/ion defined by a sequence string, parsed sequence, chemical formula or Composition object.

Note that if a sequence string without terminal groups is supplied then the isotopic composition is calculated for a polypeptide with standard terminal groups (H- and -OH).

For each element, only two most abundant isotopes are considered.

Parameters:

formula (str, optional) – A string with a chemical formula.
sequence (str, optional) – A polypeptide sequence string in modX notation.
parsed_sequence (list of str, optional) – A polypeptide sequence parsed into a list of amino acids.
composition (Composition, optional) – A Composition object with the elemental composition of a substance.
elements_with_isotopes (list of str) – A list of elements to be considered in isotopic distribution (by default, every element has a isotopic distribution).
aa_comp (dict, optional) – A dict with the elemental composition of the amino acids (the default value is std_aa_comp).
mass_data (dict, optional) – A dict with the masses of chemical elements (the default value is nist_mass).
ion_comp (dict, optional) – A dict with the relative elemental compositions of peptide ion fragments (default is std_ion_comp).

Returns:

out – A tuple with the most probable isotopic composition and its relative abundance.

Return type:

tuple (Composition, float)

pyteomics.mass.mass.nist_mass = {'Ac': {0: (227, 1.0), 206: (206.0145, 0.0), 207: (207.01195, 0.0), 208: (208.01155, 0.0), 209: (209.00949, 0.0), 210: (210.00944, 0.0), 211: (211.00773, 0.0), 212: (212.00781, 0.0), 213: (213.00661, 0.0), 214: (214.006902, 0.0), 215: (215.006454, 0.0), 216: (216.00872, 0.0), 217: (217.009347, 0.0), 218: (218.01164, 0.0), 219: (219.01242, 0.0), 220: (220.014763, 0.0), 221: (221.01559, 0.0), 222: (222.017844, 0.0), 223: (223.019137, 0.0), 224: (224.021723, 0.0), 225: (225.02323, 0.0), 226: (226.026098, 0.0), 227: (227.0277521, 0.0), 228: (228.0310211, 0.0), 229: (229.03302, 0.0), 230: (230.03629, 0.0), 231: (231.03856, 0.0), 232: (232.04203, 0.0), 233: (233.04455, 0.0), 234: (234.04842, 0.0), 235: (235.05123, 0.0), 236: (236.0553, 0.0)}, 'Ag': {0: (106.905097, 1.0), 93: (92.94978, 0.0), 94: (93.94278, 0.0), 95: (94.93548, 0.0), 96: (95.93068, 0.0), 97: (96.92397, 0.0), 98: (97.92157, 0.0), 99: (98.9176, 0.0), 100: (99.9161, 0.0), 101: (100.9128, 0.0), 102: (101.91169, 0.0), 103: (102.908973, 0.0), 104: (103.908629, 0.0), 105: (104.906529, 0.0), 106: (105.906669, 0.0), 107: (106.905097, 0.51839), 108: (107.905956, 0.0), 109: (108.904752, 0.48161), 110: (109.906107, 0.0), 111: (110.905291, 0.0), 112: (111.907005, 0.0), 113: (112.906567, 0.0), 114: (113.908804, 0.0), 115: (114.90876, 0.0), 116: (115.91136, 0.0), 117: (116.91168, 0.0), 118: (117.91458, 0.0), 119: (118.91567, 0.0), 120: (119.91879, 0.0), 121: (120.91985, 0.0), 122: (121.92353, 0.0), 123: (122.9249, 0.0), 124: (123.92864, 0.0), 125: (124.93043, 0.0), 126: (125.9345, 0.0), 127: (126.93677, 0.0), 128: (127.94117, 0.0), 129: (128.94369, 0.0), 130: (129.95045, 0.0)}, 'Al': {0: (26.98153863, 1.0), 21: (21.02804, 0.0), 22: (22.01952, 0.0), 23: (23.007267, 0.0), 24: (23.9999389, 0.0), 25: (24.9904281, 0.0), 26: (25.98689169, 0.0), 27: (26.98153863, 1.0), 28: (27.98191031, 0.0), 29: (28.980445, 0.0), 30: (29.98296, 0.0), 31: (30.983947, 0.0), 32: (31.98812, 0.0), 33: (32.99084, 0.0), 34: (33.99685, 0.0), 35: (34.99986, 0.0), 36: (36.00621, 0.0), 37: (37.01068, 0.0), 38: (38.01723, 0.0), 39: (39.02297, 0.0), 40: (40.03145, 0.0), 41: (41.03833, 0.0), 42: (42.04689, 0.0)}, 'Am': {0: (243, 1.0), 231: (231.04556, 0.0), 232: (232.04659, 0.0), 233: (233.04635, 0.0), 234: (234.04781, 0.0), 235: (235.04795, 0.0), 236: (236.04958, 0.0), 237: (237.05, 0.0), 238: (238.05198, 0.0), 239: (239.0530245, 0.0), 240: (240.0553, 0.0), 241: (241.0568291, 0.0), 242: (242.0595492, 0.0), 243: (243.0613811, 0.0), 244: (244.0642848, 0.0), 245: (245.066452, 0.0), 246: (246.069775, 0.0), 247: (247.07209, 0.0), 248: (248.07575, 0.0), 249: (249.07848, 0.0)}, 'Ar': {0: (39.9623831225, 1.0), 30: (30.02156, 0.0), 31: (31.01212, 0.0), 32: (31.997638, 0.0), 33: (32.9899257, 0.0), 34: (33.9802712, 0.0), 35: (34.9752576, 0.0), 36: (35.967545106, 0.003365), 37: (36.96677632, 0.0), 38: (37.9627324, 0.000632), 39: (38.964313, 0.0), 40: (39.9623831225, 0.996003), 41: (40.9645006, 0.0), 42: (41.963046, 0.0), 43: (42.965636, 0.0), 44: (43.964924, 0.0), 45: (44.96804, 0.0), 46: (45.96809, 0.0), 47: (46.97219, 0.0), 48: (47.97454, 0.0), 49: (48.98052, 0.0), 50: (49.98443, 0.0), 51: (50.99163, 0.0), 52: (51.99678, 0.0), 53: (53.00494, 0.0)}, 'As': {0: (74.9215965, 1.0), 60: (59.99313, 0.0), 61: (60.98062, 0.0), 62: (61.9732, 0.0), 63: (62.96369, 0.0), 64: (63.95757, 0.0), 65: (64.94956, 0.0), 66: (65.94471, 0.0), 67: (66.93919, 0.0), 68: (67.93677, 0.0), 69: (68.93227, 0.0), 70: (69.93092, 0.0), 71: (70.927112, 0.0), 72: (71.926752, 0.0), 73: (72.923825, 0.0), 74: (73.9239287, 0.0), 75: (74.9215965, 1.0), 76: (75.922394, 0.0), 77: (76.9206473, 0.0), 78: (77.921827, 0.0), 79: (78.920948, 0.0), 80: (79.922534, 0.0), 81: (80.922132, 0.0), 82: (81.9245, 0.0), 83: (82.92498, 0.0), 84: (83.92906, 0.0), 85: (84.93202, 0.0), 86: (85.9365, 0.0), 87: (86.9399, 0.0), 88: (87.94494, 0.0), 89: (88.94939, 0.0), 90: (89.9555, 0.0), 91: (90.96043, 0.0), 92: (91.9668, 0.0)}, 'At': {0: (210, 1.0), 193: (192.99984, 0.0), 194: (193.99873, 0.0), 195: (194.996268, 0.0), 196: (195.99579, 0.0), 197: (196.99319, 0.0), 198: (197.99284, 0.0), 199: (198.99053, 0.0), 200: (199.990351, 0.0), 201: (200.988417, 0.0), 202: (201.98863, 0.0), 203: (202.986942, 0.0), 204: (203.987251, 0.0), 205: (204.986074, 0.0), 206: (205.986667, 0.0), 207: (206.985784, 0.0), 208: (207.98659, 0.0), 209: (208.986173, 0.0), 210: (209.987148, 0.0), 211: (210.9874963, 0.0), 212: (211.990745, 0.0), 213: (212.992937, 0.0), 214: (213.996372, 0.0), 215: (214.998653, 0.0), 216: (216.002423, 0.0), 217: (217.004719, 0.0), 218: (218.008694, 0.0), 219: (219.011162, 0.0), 220: (220.01541, 0.0), 221: (221.01805, 0.0), 222: (222.02233, 0.0), 223: (223.02519, 0.0)}, 'Au': {0: (196.9665687, 1.0), 169: (168.99808, 0.0), 170: (169.99612, 0.0), 171: (170.991879, 0.0), 172: (171.99004, 0.0), 173: (172.986237, 0.0), 174: (173.98476, 0.0), 175: (174.98127, 0.0), 176: (175.9801, 0.0), 177: (176.976865, 0.0), 178: (177.97603, 0.0), 179: (178.973213, 0.0), 180: (179.972521, 0.0), 181: (180.970079, 0.0), 182: (181.969618, 0.0), 183: (182.967593, 0.0), 184: (183.967452, 0.0), 185: (184.965789, 0.0), 186: (185.965953, 0.0), 187: (186.964568, 0.0), 188: (187.965324, 0.0), 189: (188.963948, 0.0), 190: (189.9647, 0.0), 191: (190.9637, 0.0), 192: (191.964813, 0.0), 193: (192.96415, 0.0), 194: (193.965365, 0.0), 195: (194.9650346, 0.0), 196: (195.96657, 0.0), 197: (196.9665687, 1.0), 198: (197.9682423, 0.0), 199: (198.9687652, 0.0), 200: (199.97073, 0.0), 201: (200.971657, 0.0), 202: (201.97381, 0.0), 203: (202.975155, 0.0), 204: (203.97772, 0.0), 205: (204.97987, 0.0)}, 'B': {0: (11.0093054, 1.0), 6: (6.04681, 0.0), 7: (7.02992, 0.0), 8: (8.0246072, 0.0), 9: (9.0133288, 0.0), 10: (10.012937, 0.199), 11: (11.0093054, 0.801), 12: (12.0143521, 0.0), 13: (13.0177802, 0.0), 14: (14.025404, 0.0), 15: (15.031103, 0.0), 16: (16.03981, 0.0), 17: (17.04699, 0.0), 18: (18.05617, 0.0), 19: (19.06373, 0.0)}, 'Ba': {0: 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(126.9052263, 0.0), 128: (127.9044631, 0.3174), 129: (128.9065982, 0.0), 130: (129.9062244, 0.3408), 131: (130.9085239, 0.0), 132: (131.908553, 0.0), 133: (132.910955, 0.0), 134: (133.911369, 0.0), 135: (134.91645, 0.0), 136: (135.9201, 0.0), 137: (136.92532, 0.0), 138: (137.92922, 0.0), 139: (138.93473, 0.0), 140: (139.93885, 0.0), 141: (140.94465, 0.0), 142: (141.94908, 0.0)}, 'Th': {0: (232.0380553, 1.0), 209: (209.01772, 0.0), 210: (210.015075, 0.0), 211: (211.01493, 0.0), 212: (212.01298, 0.0), 213: (213.01301, 0.0), 214: (214.0115, 0.0), 215: (215.01173, 0.0), 216: (216.011062, 0.0), 217: (217.013114, 0.0), 218: (218.013284, 0.0), 219: (219.01554, 0.0), 220: (220.015748, 0.0), 221: (221.018184, 0.0), 222: (222.018468, 0.0), 223: (223.020811, 0.0), 224: (224.021467, 0.0), 225: (225.023951, 0.0), 226: (226.024903, 0.0), 227: (227.0277041, 0.0), 228: (228.0287411, 0.0), 229: (229.031762, 0.0), 230: (230.0331338, 0.0), 231: (231.0363043, 0.0), 232: (232.0380553, 1.0), 233: (233.0415818, 0.0), 234: (234.043601, 0.0), 235: (235.04751, 0.0), 236: (236.04987, 0.0), 237: (237.05389, 0.0), 238: (238.0565, 0.0)}, 'Ti': {0: (47.9479463, 1.0), 38: (38.00977, 0.0), 39: (39.00161, 0.0), 40: (39.9905, 0.0), 41: (40.98315, 0.0), 42: (41.973031, 0.0), 43: (42.968522, 0.0), 44: (43.9596901, 0.0), 45: (44.9581256, 0.0), 46: (45.9526316, 0.0825), 47: (46.9517631, 0.0744), 48: (47.9479463, 0.7372), 49: (48.94787, 0.0541), 50: (49.9447912, 0.0518), 51: (50.946615, 0.0), 52: (51.946897, 0.0), 53: (52.94973, 0.0), 54: (53.95105, 0.0), 55: (54.95527, 0.0), 56: (55.9582, 0.0), 57: (56.96399, 0.0), 58: (57.96697, 0.0), 59: (58.97293, 0.0), 60: (59.97676, 0.0), 61: (60.9832, 0.0), 62: (61.98749, 0.0), 63: (62.99442, 0.0)}, 'Tl': {0: (204.9744275, 1.0), 176: (176.00059, 0.0), 177: (176.996427, 0.0), 178: (177.9949, 0.0), 179: (178.99109, 0.0), 180: (179.98991, 0.0), 181: (180.986257, 0.0), 182: (181.98567, 0.0), 183: (182.982193, 0.0), 184: (183.98187, 0.0), 185: (184.97879, 0.0), 186: (185.97833, 0.0), 187: (186.975906, 0.0), 188: (187.97601, 0.0), 189: (188.973588, 0.0), 190: (189.97388, 0.0), 191: (190.971786, 0.0), 192: (191.97223, 0.0), 193: (192.97067, 0.0), 194: (193.9712, 0.0), 195: (194.969774, 0.0), 196: (195.970481, 0.0), 197: (196.969575, 0.0), 198: (197.97048, 0.0), 199: (198.96988, 0.0), 200: (199.970963, 0.0), 201: (200.970819, 0.0), 202: (201.972106, 0.0), 203: (202.9723442, 0.2952), 204: (203.9738635, 0.0), 205: (204.9744275, 0.7048), 206: (205.9761103, 0.0), 207: (206.977419, 0.0), 208: (207.9820187, 0.0), 209: (208.985359, 0.0), 210: (209.990074, 0.0), 211: (210.99348, 0.0), 212: (211.99823, 0.0)}, 'Tm': {0: (168.9342133, 1.0), 145: (144.97007, 0.0), 146: (145.96643, 0.0), 147: (146.96096, 0.0), 148: (147.95784, 0.0), 149: (148.95272, 0.0), 150: (149.94996, 0.0), 151: (150.945483, 0.0), 152: (151.94442, 0.0), 153: (152.942012, 0.0), 154: (153.941568, 0.0), 155: (154.939199, 0.0), 156: (155.93898, 0.0), 157: (156.93697, 0.0), 158: (157.93698, 0.0), 159: (158.93498, 0.0), 160: (159.93526, 0.0), 161: (160.93355, 0.0), 162: (161.933995, 0.0), 163: (162.932651, 0.0), 164: (163.93356, 0.0), 165: (164.932435, 0.0), 166: (165.933554, 0.0), 167: (166.9328516, 0.0), 168: (167.934173, 0.0), 169: (168.9342133, 1.0), 170: (169.9358014, 0.0), 171: (170.9364294, 0.0), 172: (171.9384, 0.0), 173: (172.939604, 0.0), 174: (173.94217, 0.0), 175: (174.94384, 0.0), 176: (175.94699, 0.0), 177: (176.94904, 0.0), 178: (177.95264, 0.0), 179: (178.95534, 0.0)}, 'U': {0: (238.0507882, 1.0), 217: (217.02437, 0.0), 218: (218.02354, 0.0), 219: (219.02492, 0.0), 220: (220.02472, 0.0), 221: (221.0264, 0.0), 222: (222.02609, 0.0), 223: (223.02774, 0.0), 224: (224.027605, 0.0), 225: (225.029391, 0.0), 226: (226.029339, 0.0), 227: (227.031156, 0.0), 228: (228.031374, 0.0), 229: (229.033506, 0.0), 230: (230.03394, 0.0), 231: (231.036294, 0.0), 232: (232.0371562, 0.0), 233: (233.0396352, 0.0), 234: (234.0409521, 5.4e-05), 235: (235.0439299, 0.007204), 236: (236.045568, 0.0), 237: (237.0487302, 0.0), 238: (238.0507882, 0.992742), 239: (239.0542933, 0.0), 240: (240.056592, 0.0), 241: (241.06033, 0.0), 242: (242.06293, 0.0)}, 'Uuh': {0: (293, 1.0), 289: (289.19886, 0.0), 290: (290.19859, 0.0), 291: (291.20001, 0.0), 292: (292.19979, 0.0)}, 'Uuo': {0: (294, 1.0), 293: (293.21467, 0.0)}, 'Uup': {0: (288, 1.0), 287: (287.19119, 0.0), 288: (288.19249, 0.0), 289: (289.19272, 0.0), 290: (290.19414, 0.0), 291: (291.19438, 0.0)}, 'Uuq': {0: (289, 1.0), 285: (285.1837, 0.0), 286: (286.18386, 0.0), 287: (287.1856, 0.0), 288: (288.18569, 0.0), 289: (289.18728, 0.0)}, 'Uus': {0: (292, 1.0), 291: (291.20656, 0.0), 292: (292.20755, 0.0)}, 'Uut': {0: (284, 1.0), 283: (283.17645, 0.0), 284: (284.17808, 0.0), 285: (285.17873, 0.0), 286: (286.18048, 0.0), 287: (287.18105, 0.0)}, 'V': {0: (50.9439595, 1.0), 40: (40.01109, 0.0), 41: (40.99978, 0.0), 42: (41.99123, 0.0), 43: (42.98065, 0.0), 44: (43.97411, 0.0), 45: (44.965776, 0.0), 46: (45.9602005, 0.0), 47: (46.9549089, 0.0), 48: (47.9522537, 0.0), 49: (48.9485161, 0.0), 50: (49.9471585, 0.0025), 51: (50.9439595, 0.9975), 52: (51.9447755, 0.0), 53: (52.944338, 0.0), 54: (53.94644, 0.0), 55: (54.94723, 0.0), 56: (55.95053, 0.0), 57: (56.95256, 0.0), 58: (57.95683, 0.0), 59: (58.96021, 0.0), 60: (59.96503, 0.0), 61: (60.96848, 0.0), 62: (61.97378, 0.0), 63: (62.97755, 0.0), 64: (63.98347, 0.0), 65: (64.98792, 0.0)}, 'W': {0: (183.9509312, 1.0), 158: (157.97456, 0.0), 159: (158.97292, 0.0), 160: (159.96848, 0.0), 161: (160.96736, 0.0), 162: (161.963497, 0.0), 163: (162.96252, 0.0), 164: (163.958954, 0.0), 165: (164.95828, 0.0), 166: (165.955027, 0.0), 167: (166.954816, 0.0), 168: (167.951808, 0.0), 169: (168.951779, 0.0), 170: (169.949228, 0.0), 171: (170.94945, 0.0), 172: (171.94729, 0.0), 173: (172.94769, 0.0), 174: (173.94608, 0.0), 175: (174.94672, 0.0), 176: (175.94563, 0.0), 177: (176.94664, 0.0), 178: (177.945876, 0.0), 179: (178.94707, 0.0), 180: (179.946704, 0.0012), 181: (180.948197, 0.0), 182: (181.9482042, 0.265), 183: (182.950223, 0.1431), 184: (183.9509312, 0.3064), 185: (184.9534193, 0.0), 186: (185.9543641, 0.2843), 187: (186.9571605, 0.0), 188: (187.958489, 0.0), 189: (188.96191, 0.0), 190: (189.96318, 0.0), 191: (190.9666, 0.0), 192: (191.96817, 0.0)}, 'Xe': {0: (131.9041535, 1.0), 110: (109.94428, 0.0), 111: (110.9416, 0.0), 112: (111.93562, 0.0), 113: (112.93334, 0.0), 114: (113.92798, 0.0), 115: (114.926294, 0.0), 116: (115.921581, 0.0), 117: (116.920359, 0.0), 118: (117.916179, 0.0), 119: (118.915411, 0.0), 120: (119.911784, 0.0), 121: (120.911462, 0.0), 122: (121.908368, 0.0), 123: (122.908482, 0.0), 124: (123.905893, 0.000952), 125: (124.9063955, 0.0), 126: (125.904274, 0.00089), 127: (126.905184, 0.0), 128: (127.9035313, 0.019102), 129: (128.9047794, 0.264006), 130: (129.903508, 0.04071), 131: (130.9050824, 0.212324), 132: (131.9041535, 0.269086), 133: (132.9059107, 0.0), 134: (133.9053945, 0.104357), 135: (134.907227, 0.0), 136: (135.907219, 0.088573), 137: (136.911562, 0.0), 138: (137.91395, 0.0), 139: (138.918793, 0.0), 140: (139.92164, 0.0), 141: (140.92665, 0.0), 142: (141.92971, 0.0), 143: (142.93511, 0.0), 144: (143.93851, 0.0), 145: (144.94407, 0.0), 146: (145.94775, 0.0), 147: (146.95356, 0.0)}, 'Y': {0: (88.9058483, 1.0), 76: (75.95845, 0.0), 77: (76.94965, 0.0), 78: (77.94361, 0.0), 79: (78.93735, 0.0), 80: (79.93428, 0.0), 81: (80.92913, 0.0), 82: (81.92679, 0.0), 83: (82.92235, 0.0), 84: (83.92039, 0.0), 85: (84.916433, 0.0), 86: (85.914886, 0.0), 87: (86.9108757, 0.0), 88: (87.9095011, 0.0), 89: (88.9058483, 1.0), 90: (89.9071519, 0.0), 91: (90.907305, 0.0), 92: (91.908949, 0.0), 93: (92.909583, 0.0), 94: (93.911595, 0.0), 95: (94.912821, 0.0), 96: (95.915891, 0.0), 97: (96.918134, 0.0), 98: (97.922203, 0.0), 99: (98.924636, 0.0), 100: (99.92776, 0.0), 101: (100.93031, 0.0), 102: (101.93356, 0.0), 103: (102.93673, 0.0), 104: (103.94105, 0.0), 105: (104.94487, 0.0), 106: (105.94979, 0.0), 107: (106.95414, 0.0), 108: (107.95948, 0.0)}, 'Yb': {0: (173.9388621, 1.0), 148: (147.96742, 0.0), 149: (148.96404, 0.0), 150: (149.95842, 0.0), 151: (150.9554, 0.0), 152: (151.95029, 0.0), 153: (152.94948, 0.0), 154: (153.946394, 0.0), 155: (154.945782, 0.0), 156: (155.942818, 0.0), 157: (156.942628, 0.0), 158: (157.939866, 0.0), 159: (158.94005, 0.0), 160: (159.937552, 0.0), 161: (160.937902, 0.0), 162: (161.935768, 0.0), 163: (162.936334, 0.0), 164: (163.934489, 0.0), 165: (164.93528, 0.0), 166: (165.933882, 0.0), 167: (166.93495, 0.0), 168: (167.933897, 0.0013), 169: (168.93519, 0.0), 170: (169.9347618, 0.0304), 171: (170.9363258, 0.1428), 172: (171.9363815, 0.2183), 173: (172.9382108, 0.1613), 174: (173.9388621, 0.3183), 175: (174.9412765, 0.0), 176: (175.9425717, 0.1276), 177: (176.9452608, 0.0), 178: (177.946647, 0.0), 179: (178.95017, 0.0), 180: (179.95233, 0.0), 181: (180.95615, 0.0)}, 'Zn': {0: (63.9291422, 1.0), 54: (53.99295, 0.0), 55: (54.98398, 0.0), 56: (55.97238, 0.0), 57: (56.96479, 0.0), 58: (57.95459, 0.0), 59: (58.94926, 0.0), 60: (59.941827, 0.0), 61: (60.939511, 0.0), 62: (61.93433, 0.0), 63: (62.9332116, 0.0), 64: (63.9291422, 0.48268), 65: (64.929241, 0.0), 66: (65.9260334, 0.27975), 67: (66.9271273, 0.04102), 68: (67.9248442, 0.19024), 69: (68.9265503, 0.0), 70: (69.9253193, 0.00631), 71: (70.927722, 0.0), 72: (71.926858, 0.0), 73: (72.92978, 0.0), 74: (73.92946, 0.0), 75: (74.93294, 0.0), 76: (75.93329, 0.0), 77: (76.93696, 0.0), 78: (77.93844, 0.0), 79: (78.94265, 0.0), 80: (79.94434, 0.0), 81: (80.95048, 0.0), 82: (81.95442, 0.0), 83: (82.96103, 0.0)}, 'Zr': {0: (89.9047044, 1.0), 78: (77.95523, 0.0), 79: (78.94916, 0.0), 80: (79.9404, 0.0), 81: (80.93721, 0.0), 82: (81.93109, 0.0), 83: (82.92865, 0.0), 84: (83.92325, 0.0), 85: (84.92147, 0.0), 86: (85.91647, 0.0), 87: (86.914816, 0.0), 88: (87.910227, 0.0), 89: (88.90889, 0.0), 90: (89.9047044, 0.5145), 91: (90.9056458, 0.1122), 92: (91.9050408, 0.1715), 93: (92.906476, 0.0), 94: (93.9063152, 0.1738), 95: (94.9080426, 0.0), 96: (95.9082734, 0.028), 97: (96.9109531, 0.0), 98: (97.912735, 0.0), 99: (98.916512, 0.0), 100: (99.91776, 0.0), 101: (100.92114, 0.0), 102: (101.92298, 0.0), 103: (102.9266, 0.0), 104: (103.92878, 0.0), 105: (104.93305, 0.0), 106: (105.93591, 0.0), 107: (106.94075, 0.0), 108: (107.94396, 0.0), 109: (108.94924, 0.0), 110: (109.95287, 0.0)}, 'e*': {0: (0.00054857990943, 1.0)}, 'e-': {0: (0.00054857990943, 1.0)}}¶: A dict with the exact element masses downloaded from the NIST website: http://www.nist.gov/pml/data/comp.cfm . There are entries for each element containing the masses and relative abundances of several abundant isotopes and a separate entry for undefined isotope with zero key, mass of the most abundant isotope and 1.0 abundance.

pyteomics.mass.mass.std_aa_comp = {'-OH': {'H': 1, 'O': 1}, 'A': {'C': 3, 'H': 5, 'N': 1, 'O': 1}, 'C': {'C': 3, 'H': 5, 'N': 1, 'O': 1, 'S': 1}, 'D': {'C': 4, 'H': 5, 'N': 1, 'O': 3}, 'E': {'C': 5, 'H': 7, 'N': 1, 'O': 3}, 'F': {'C': 9, 'H': 9, 'N': 1, 'O': 1}, 'G': {'C': 2, 'H': 3, 'N': 1, 'O': 1}, 'H': {'C': 6, 'H': 7, 'N': 3, 'O': 1}, 'H-': {'H': 1}, 'I': {'C': 6, 'H': 11, 'N': 1, 'O': 1}, 'J': {'C': 6, 'H': 11, 'N': 1, 'O': 1}, 'K': {'C': 6, 'H': 12, 'N': 2, 'O': 1}, 'L': {'C': 6, 'H': 11, 'N': 1, 'O': 1}, 'M': {'C': 5, 'H': 9, 'N': 1, 'O': 1, 'S': 1}, 'N': {'C': 4, 'H': 6, 'N': 2, 'O': 2}, 'O': {'C': 12, 'H': 19, 'N': 3, 'O': 2}, 'P': {'C': 5, 'H': 7, 'N': 1, 'O': 1}, 'Q': {'C': 5, 'H': 8, 'N': 2, 'O': 2}, 'R': {'C': 6, 'H': 12, 'N': 4, 'O': 1}, 'S': {'C': 3, 'H': 5, 'N': 1, 'O': 2}, 'T': {'C': 4, 'H': 7, 'N': 1, 'O': 2}, 'U': {'C': 3, 'H': 5, 'N': 1, 'O': 1, 'Se': 1}, 'V': {'C': 5, 'H': 9, 'N': 1, 'O': 1}, 'W': {'C': 11, 'H': 10, 'N': 2, 'O': 1}, 'Y': {'C': 9, 'H': 9, 'N': 1, 'O': 2}}¶: A dictionary with elemental compositions of the twenty standard amino acid residues, selenocysteine, pyrrolysine, and standard H- and -OH terminal groups.

pyteomics.mass.mass.std_aa_mass = {'A': 71.03711378471, 'C': 103.00918478471, 'D': 115.02694302383001, 'E': 129.04259308796998, 'F': 147.06841391298997, 'G': 57.02146372057, 'H': 137.05891185845002, 'I': 113.08406397713001, 'J': 113.08406397713001, 'K': 128.09496301399997, 'L': 113.08406397713001, 'M': 131.04048491299, 'N': 114.04292744114001, 'O': 237.14772686284996, 'P': 97.05276384885, 'Q': 128.05857750527997, 'R': 156.10111102359997, 'S': 87.03202840427001, 'T': 101.04767846841, 'U': 150.95363508471, 'V': 99.06841391299, 'W': 186.07931294985997, 'Y': 163.06332853254997}¶: A dictionary with monoisotopic masses of the twenty standard amino acid residues, selenocysteine and pyrrolysine.

pyteomics.mass.mass.std_ion_comp = {'M': {}, 'M-H2O': {'H': -2, 'O': -1}, 'M-NH3': {'H': -3, 'N': -1}, 'a': {'C': -1, 'H': -2, 'O': -2}, 'a+1': {'C': -1, 'H': -1, 'O': -2}, 'a-H2O': {'C': -1, 'H': -4, 'O': -3}, 'a-NH3': {'C': -1, 'H': -5, 'N': -1, 'O': -2}, 'b': {'H': -2, 'O': -1}, 'b-H2O': {'H': -4, 'O': -2}, 'b-NH3': {'H': -5, 'N': -1, 'O': -1}, 'c': {'H': 1, 'N': 1, 'O': -1}, 'c+1': {'H': 2, 'N': 1, 'O': -1}, 'c+2': {'H': 3, 'N': 1, 'O': -1}, 'c-1': {'N': 1, 'O': -1}, 'c-H2O': {'H': -1, 'N': 1, 'O': -2}, 'c-NH3': {'H': -2, 'O': -1}, 'c-dot': {'H': 2, 'N': 1, 'O': -1}, 'x': {'C': 1, 'H': -2, 'O': 1}, 'x+1': {'C': 1, 'H': -1, 'O': 1}, 'x-H2O': {'C': 1, 'H': -4}, 'x-NH3': {'C': 1, 'H': -5, 'N': -1, 'O': 1}, 'y': {}, 'y-H2O': {'H': -2, 'O': -1}, 'y-NH3': {'H': -3, 'N': -1}, 'z': {'H': -3, 'N': -1}, 'z+1': {'H': -2, 'N': -1}, 'z+2': {'H': -1, 'N': -1}, 'z+3': {'N': -1}, 'z-1': {'H': -4, 'N': -1}, 'z-H2O': {'H': -5, 'N': -1, 'O': -1}, 'z-NH3': {'H': -6, 'N': -2}, 'z-dot': {'H': -2, 'N': -1}}¶: A dict with relative elemental compositions of the standard peptide fragment ions. An elemental composition of a fragment ion is calculated as a difference between the total elemental composition of an ion and the sum of elemental compositions of its constituting amino acid residues.

Pyteomics documentation v5.0rc2